Organize Files

Restructure the shared notes directory so every agent can find what they need quickly.

For a complete before/after walkthrough on a realistic messy notes/ tree — including the dedup pass, naming fixes, subdirectory creation, link repair, and audit-log entry — see references/worked-example.md. Read it once before your first reorganization; it makes the abstract steps below concrete.

For recovery procedures and judgment calls (move script aborted partway, false-positive duplicates, files that look misplaced in _synthesis/, contradicting _open-questions.md, races between agents…), see references/edge-cases.md.

When to Use

• Too many flat files in research/ or experiments/
• Duplicate or near-duplicate notes
• Inconsistent naming (spaces, uppercase, agent IDs in filenames)
• After a deep-research or consolidate phase that created many files
• You can't find a note you know exists

Notes Directory Structure

notes/
├── index.md          ← table of contents (research + experiments only)
├── raw/              ← immutable sources (DON'T touch)
├── research/         ← deep-research findings (organize within)
│   ├── <topic>/      ← group by topic or theme
│   └── ...
├── experiments/      ← eval reflections and results (organize within)
│   ├── <approach>/   ← group by approach or technique
│   └── ...
├── _synthesis/       ← consolidate owns this (DON'T touch)
├── _connections.md   ← consolidate owns this
├── _open-questions.md
└── _organization-log.md  ← append-only log of what you changed

Process

1. Audit

Get the current state:

bash .coral/public/skills/organize-files/scripts/audit.sh

Or manually: ls -R {shared_dir}/notes/ and count files per directory.

Also check for content-level issues:

• Contradictions — do any notes claim opposite things? Update or flag them in _open-questions.md.
• Stale info — research notes that experiments have disproven. Update with actual results.
• Orphan pages — notes not listed in index.md. Add them.
• Missing cross-references — related notes that don't link to each other.
• Gaps — techniques mentioned but never researched, or researched but never tried.

2. Plan

Write out your target structure before moving anything. Organize within research/ and experiments/ — add subdirectories by topic when a dir has 5+ files:

research/
├── algorithms/       (3+ notes)
├── optimization/     (3+ notes)
└── ...

experiments/
├── optimization/     (3+ notes)
├── debugging/        (3+ notes)
└── ...

Rules:

• Minimum 3 files per subdirectory — don't create a dir for 1-2 files
• Max 2 levels deep — experiments/optimization/learning-rate.md is the limit
• Name by topic — algorithms/ not agent1-work/
• Don't touch raw/ — immutable source material
• Don't touch _synthesis/, _connections.md, _open-questions.md — owned by consolidate
• Don't touch research/_coverage.md — the research coverage ledger, owned by the research team (the _ prefix already keeps the index/dedup/link scripts off it)

3. Deduplicate

Find near-duplicates:

python .coral/public/skills/organize-files/scripts/find_duplicates.py .coral/public/notes --threshold 0.5

For pairs above the threshold where the verdict is not immediately obvious from a quick read — same topic vs. different angle vs. different topic with shared boilerplate vs. genuinely contradicting — spawn the Dedup Judge subagent. It reads both notes blinded (no author / timestamp / length metadata) and returns a structured verdict (same-topic-merge / different-angle-fold / contradicting-do-not-merge / keep-both-rename) with concrete merge or rename instructions. See agents/dedup-judge.md. Use it especially when:

• The two notes were written by different agents (recency / author bias is highest).
• One note is much longer than the other (length bias makes the long one feel authoritative).
• The notes appear to disagree but you can't tell if it's a real conflict or a scope difference.

For obvious cases — verbatim duplicates, or clearly different topics that shared a paragraph — just decide directly.

When merging confirmed duplicates, preserve provenance from both notes — never just pick one and discard:

• Union the ## References lists (de-duplicated by URL or raw/ filename). Losing a citation loses an audit trail that an agent may need months later.
• Keep the more specific claims from each note, not just whichever was longer. A short note with concrete numbers usually has higher information density than a long one with vague prose.
• Combine tags and aliases rather than picking one set. Both were correct in their original context.

Move originals to _archive/ so the merge is reversible.

When two notes contradict each other, don't merge:

• Flag the conflict in _open-questions.md (existing rule).
• Also stamp contradictedBy: [other-note-slug] into each note's frontmatter so future readers see the conflict at the note level — _open-questions.md collects them, but agents reading the note directly should see the warning without a separate lookup.

4. Move and Rename

Use the move script for safe moves with frontmatter tracking:

python .coral/public/skills/organize-files/scripts/move_note.py SOURCE DEST

Naming: kebab-case-like-this.md, topic first, no agent IDs, no bare dates, under 60 chars.

5. Update Index

Regenerate index.md:

python .coral/public/skills/organize-files/scripts/generate_index.py .coral/public/notes

The index should only list research/ and experiments/ entries — not raw/.

Then resolve cross-links — moves and renames break any [[old-slug]] references in note bodies:

python .coral/public/skills/organize-files/scripts/resolve_links.py .coral/public/notes --dry-run
# review the diff, then:
python .coral/public/skills/organize-files/scripts/resolve_links.py .coral/public/notes

The resolver walks every note, scans the body for plain-text mentions of every other note's title, and wraps them as [[slug|Title]]. It skips text already inside wikilinks, citation markers, code blocks, and inline code. Run this after moves and renames, not before — the resolver needs final paths.

6. Log

Append a summary to _organization-log.md: what you moved, merged, or renamed, and why.